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Example
An example set of input sequences (for Hepatitis B virus) is included
in the distribution. To run the example, do the following:
> cd EXAMPLE1
> ./run_mlrgd hbv
(Note that a few of the parameters in EXAMPLE1/run_mlrgd differ
from those in the default run_mlrgd - e.g. the circular
genome option is switched on.)
The programme produces a number of output files, which will be
described in more detail below. The file hbv.fcm.eps (Figure
1; postscript image; view with e.g. ggv
hbv.fcm.eps) shows a number of statistics and conservation plots
(running mean) for non-coding positions, 1st, 2nd and 3rd codon
positions, four-fold degenerate neutral sites, and all nucleotide
positions. There are other tracks for the estimated
-values,
the number of contributing sequences in each column (i.e. not gapped in the alignment), annotated CDSs, and any other annotated
features (here the annotated features are from Smith et al. 1998,
Moolla et al. 2002, Chen et al. 2005, and the NCBI reference
sequence NC_003977).
There is another example (Barley Yellow Dwarf Virus), using
GENBANK-format sequences, in EXAMPLE2:
> cd EXAMPLE2
> ./run_mlrgd bydv
In general the command is
> ./run_mlrgd prefix
Figure 1:
One of the output plots for Hepatitis B Virus
example.
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Next: Required software and files
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aef
2007-12-10